1
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Widmalm G. Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy. JACS AU 2024; 4:20-39. [PMID: 38274261 PMCID: PMC10807006 DOI: 10.1021/jacsau.3c00639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024]
Abstract
Glycans in the form of oligosaccharides, polysaccharides, and glycoconjugates are ubiquitous in nature, and their structures range from linear assemblies to highly branched and decorated constructs. Solution state NMR spectroscopy facilitates elucidation of preferred conformations and shapes of the saccharides, motions, and dynamic aspects related to processes over time as well as the study of transient interactions with proteins. Identification of intermolecular networks at the atomic level of detail in recognition events by carbohydrate-binding proteins known as lectins, unraveling interactions with antibodies, and revealing substrate scope and action of glycosyl transferases employed for synthesis of oligo- and polysaccharides may efficiently be analyzed by NMR spectroscopy. By utilizing NMR active nuclei present in glycans and derivatives thereof, including isotopically enriched compounds, highly detailed information can be obtained by the experiments. Subsequent analysis may be aided by quantum chemical calculations of NMR parameters, machine learning-based methodologies and artificial intelligence. Interpretation of the results from NMR experiments can be complemented by extensive molecular dynamics simulations to obtain three-dimensional dynamic models, thereby clarifying molecular recognition processes involving the glycans.
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Affiliation(s)
- Göran Widmalm
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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2
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Necelis M, McDermott C, Belcher Dufrisne M, Baryiames C, Columbus L. Solution NMR investigations of integral membrane proteins: Challenges and innovations. Curr Opin Struct Biol 2023; 82:102654. [PMID: 37542910 PMCID: PMC10529709 DOI: 10.1016/j.sbi.2023.102654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/08/2023] [Accepted: 06/20/2023] [Indexed: 08/07/2023]
Abstract
Compared to soluble protein counterparts, the understanding of membrane protein stability, solvent interactions, and function are not as well understood. Recent advancements in labeling, expression, and stabilization of membrane proteins have enabled solution nuclear magnetic resonance spectroscopy to investigate membrane protein conformational states, ligand binding, lipid interactions, stability, and folding. This review highlights these advancements and new understandings and provides examples of recent applications.
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Affiliation(s)
- Matthew Necelis
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Connor McDermott
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | | | | | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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3
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Saul P, Schröder L, Schmidt AB, Hövener JB. Nanomaterials for hyperpolarized nuclear magnetic resonance and magnetic resonance imaging. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2023:e1879. [PMID: 36781151 DOI: 10.1002/wnan.1879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/03/2023] [Accepted: 01/07/2023] [Indexed: 02/15/2023]
Abstract
Nanomaterials play an important role in the development and application of hyperpolarized materials for magnetic resonance imaging (MRI). In this context they can not only act as hyperpolarized materials which are directly imaged but also play a role as carriers for hyperpolarized gases and catalysts for para-hydrogen induced polarization (PHIP) to generate hyperpolarized substrates for metabolic imaging. Those three application possibilities are discussed, focusing on carbon-based materials for the directly imaged particles. An overview over recent developments in all three fields is given, including the early developments in each field as well as important steps towards applications in MRI, such as making the initially developed methods more biocompatible and first imaging experiments with spatial resolution in either phantoms or in vivo studies. Focusing on the important features nanomaterials need to display to be applicable in the MRI context, a wide range of different approaches to that extent is covered, giving the reader a general idea of different possibilities as well as recent developments in those different fields of hyperpolarized magnetic resonance. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > In Vivo Nanodiagnostics and Imaging.
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Affiliation(s)
- Philip Saul
- Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Schleswig-Holstein, Kiel University, Kiel, Germany
| | - Leif Schröder
- Division of Translational Molecular Imaging, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany.,Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Andreas B Schmidt
- Intergrative Biosciences (Ibio), Department of Chemistry, Karmanos Cancer Institute (KCI), Wayne State University, Detroit, Michigan, USA.,German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Medical Physics, Department of Radiology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jan-Bernd Hövener
- Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Schleswig-Holstein, Kiel University, Kiel, Germany
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4
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Nishimura K, Yabuki R, Hamachi T, Kimizuka N, Tateishi K, Uesaka T, Yanai N. Dynamic Electron Polarization Lasting More Than 10 μs by Hybridizing Porphyrin and TEMPO with Flexible Linkers. J Phys Chem B 2023; 127:1219-1228. [PMID: 36717096 DOI: 10.1021/acs.jpcb.2c07936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Dynamic electron polarization (DEP), induced by quenching of photoexcited species by stable radicals, can hyperpolarize electron spins in solution at room temperature. Recently, development of technologies based on electron spin polarization such as dynamic nuclear polarization (DNP) has been progressing, where it is important to design molecules that achieve long-lasting DEP in addition to high DEP. Hybridization by linking dyes and radicals is a promising approach for efficient DEP, but strong interactions between neighboring dyes and radicals often result in the rapid decay of DEP. In this study, we introduce a flexible linker into the hybrid system of porphyrin and TEMPO to achieve both efficient DEP and long-lasting DEP. The structural flexibility of the linker switches the interaction between the radical and the triplet, which promotes the DEP process by bringing the radical and the triplet into close proximity, while avoiding abrupt relaxation due to strong interactions. As a result, the new hybridized system exhibits a larger DEP than the unlinked system, while at the same time achieving a DEP lasting more than 10 μs.
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Affiliation(s)
- Koki Nishimura
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka819-0395, Japan
| | - Reiya Yabuki
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka819-0395, Japan
| | - Tomoyuki Hamachi
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka819-0395, Japan
| | - Nobuo Kimizuka
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka819-0395, Japan
| | - Kenichiro Tateishi
- Cluster for Pioneering Research, RIKEN, RIKEN Nishina Center for Accelerator-Based Science, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
| | - Tomohiro Uesaka
- Cluster for Pioneering Research, RIKEN, RIKEN Nishina Center for Accelerator-Based Science, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
| | - Nobuhiro Yanai
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka819-0395, Japan
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5
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Eills J, Budker D, Cavagnero S, Chekmenev EY, Elliott SJ, Jannin S, Lesage A, Matysik J, Meersmann T, Prisner T, Reimer JA, Yang H, Koptyug IV. Spin Hyperpolarization in Modern Magnetic Resonance. Chem Rev 2023; 123:1417-1551. [PMID: 36701528 PMCID: PMC9951229 DOI: 10.1021/acs.chemrev.2c00534] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Magnetic resonance techniques are successfully utilized in a broad range of scientific disciplines and in various practical applications, with medical magnetic resonance imaging being the most widely known example. Currently, both fundamental and applied magnetic resonance are enjoying a major boost owing to the rapidly developing field of spin hyperpolarization. Hyperpolarization techniques are able to enhance signal intensities in magnetic resonance by several orders of magnitude, and thus to largely overcome its major disadvantage of relatively low sensitivity. This provides new impetus for existing applications of magnetic resonance and opens the gates to exciting new possibilities. In this review, we provide a unified picture of the many methods and techniques that fall under the umbrella term "hyperpolarization" but are currently seldom perceived as integral parts of the same field. Specifically, before delving into the individual techniques, we provide a detailed analysis of the underlying principles of spin hyperpolarization. We attempt to uncover and classify the origins of hyperpolarization, to establish its sources and the specific mechanisms that enable the flow of polarization from a source to the target spins. We then give a more detailed analysis of individual hyperpolarization techniques: the mechanisms by which they work, fundamental and technical requirements, characteristic applications, unresolved issues, and possible future directions. We are seeing a continuous growth of activity in the field of spin hyperpolarization, and we expect the field to flourish as new and improved hyperpolarization techniques are implemented. Some key areas for development are in prolonging polarization lifetimes, making hyperpolarization techniques more generally applicable to chemical/biological systems, reducing the technical and equipment requirements, and creating more efficient excitation and detection schemes. We hope this review will facilitate the sharing of knowledge between subfields within the broad topic of hyperpolarization, to help overcome existing challenges in magnetic resonance and enable novel applications.
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Affiliation(s)
- James Eills
- Institute
for Bioengineering of Catalonia, Barcelona
Institute of Science and Technology, 08028Barcelona, Spain,
| | - Dmitry Budker
- Johannes
Gutenberg-Universität Mainz, 55128Mainz, Germany,Helmholtz-Institut,
GSI Helmholtzzentrum für Schwerionenforschung, 55128Mainz, Germany,Department
of Physics, UC Berkeley, Berkeley, California94720, United States
| | - Silvia Cavagnero
- Department
of Chemistry, University of Wisconsin, Madison, Madison, Wisconsin53706, United States
| | - Eduard Y. Chekmenev
- Department
of Chemistry, Integrative Biosciences (IBio), Karmanos Cancer Institute
(KCI), Wayne State University, Detroit, Michigan48202, United States,Russian
Academy of Sciences, Moscow119991, Russia
| | - Stuart J. Elliott
- Molecular
Sciences Research Hub, Imperial College
London, LondonW12 0BZ, United Kingdom
| | - Sami Jannin
- Centre
de RMN à Hauts Champs de Lyon, Université
de Lyon, CNRS, ENS Lyon, Université Lyon 1, 69100Villeurbanne, France
| | - Anne Lesage
- Centre
de RMN à Hauts Champs de Lyon, Université
de Lyon, CNRS, ENS Lyon, Université Lyon 1, 69100Villeurbanne, France
| | - Jörg Matysik
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstr. 3, 04103Leipzig, Germany
| | - Thomas Meersmann
- Sir
Peter Mansfield Imaging Centre, University Park, School of Medicine, University of Nottingham, NottinghamNG7 2RD, United Kingdom
| | - Thomas Prisner
- Institute
of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic
Resonance, Goethe University Frankfurt, , 60438Frankfurt
am Main, Germany
| | - Jeffrey A. Reimer
- Department
of Chemical and Biomolecular Engineering, UC Berkeley, and Materials Science Division, Lawrence Berkeley National
Laboratory, Berkeley, California94720, United States
| | - Hanming Yang
- Department
of Chemistry, University of Wisconsin, Madison, Madison, Wisconsin53706, United States
| | - Igor V. Koptyug
- International Tomography Center, Siberian
Branch of the Russian Academy
of Sciences, 630090Novosibirsk, Russia,
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6
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Abstract
Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
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Affiliation(s)
- Carolina Fontana
- Departamento
de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden,
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7
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Flow NMR system development for real-time in situ multiple detection of direct methanol fuel cell exhausts. Electrochem commun 2022. [DOI: 10.1016/j.elecom.2022.107417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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8
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Vang JY, Breceda C, Her C, Krishnan VV. Enzyme kinetics by real-time quantitative NMR (qNMR) spectroscopy with progress curve analysis. Anal Biochem 2022; 658:114919. [PMID: 36154835 DOI: 10.1016/j.ab.2022.114919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/26/2022]
Abstract
This review article summarizes how the experimental data obtained using quantitative nuclear magnetic resonance (qNMR) spectroscopy can be combined with progress curve analysis to determine enzyme kinetic parameters. The qNMR approach enables following the enzymatic conversion of the substrate to the product in real-time by a continuous collection of spectra. The Lambert-W function, a closed-form solution to the time-dependent substrate/product kinetics of the rate equation, can estimate the Michaelis-Menten constant (KM.) and the maximum velocity (Vmax) from a single experiment. This article highlights how the qNMR data is well suited for analysis using the Lambert-W function with three different applications. Results from studies on acetylcholinesterase (acetylcholine to acetic acid and choline), β-Galactosidase (lactose to glucose and galactose), and invertase (sucrose to glucose and fructose) are presented. Furthermore, an additional example of how the progress curve analysis is applied to understand the inhibitory role of the artificial sweetener sucralose on sucrose's enzymatic conversion by invertase is discussed. With the wide availability of NMR spectrometers in academia and industries, including bench-top systems with permanent magnets, and the potential to enhance sensitivity using dynamic nuclear polarization in combination with ultrafast methods, the NMR-based enzyme kinetics could be considered a valuable tool for broader applications in the field of enzyme kinetics.
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Affiliation(s)
- Justin Y Vang
- Department of Chemistry & Biochemistry, California State University, Fresno, CA, 93740, USA
| | - Candido Breceda
- Department of Chemistry & Biochemistry, California State University, Fresno, CA, 93740, USA
| | - Cheenou Her
- Department of Chemistry & Biochemistry, California State University, Fresno, CA, 93740, USA
| | - V V Krishnan
- Department of Chemistry & Biochemistry, California State University, Fresno, CA, 93740, USA; Department of Medical Pathology & Laboratory Medicine, University of California Davis School of Medicine, Davis, CA, 95616, USA.
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9
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Optical Dynamic Nuclear Polarization of 13C Spins in Diamond at a Low Field with Multi-Tone Microwave Irradiation. Molecules 2022; 27:molecules27051700. [PMID: 35268801 PMCID: PMC8911784 DOI: 10.3390/molecules27051700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/18/2022] [Accepted: 03/02/2022] [Indexed: 11/29/2022] Open
Abstract
Majority of dynamic nuclear polarization (DNP) experiments have been requiring helium cryogenics and strong magnetic fields for a high degree of nuclear polarization. In this work, we instead demonstrate an optical hyperpolarization of naturally abundant 13C nuclei in a diamond crystal at a low magnetic field and the room temperature. It exploits continuous laser irradiation for polarizing electronic spins of nitrogen vacancy centers and microwave irradiation for transferring the electronic polarization to 13C nuclear spins. We have studied the dependence of 13C polarization on laser and microwave powers. For the first time, a triplet structure corresponding to the 14N hyperfine splitting has been observed in the 13C polarization spectrum. By simultaneously exciting three microwave frequencies at the peaks of the triplet, we have achieved 13C bulk polarization of 0.113 %, leading to an enhancement of 90,000 over the thermal polarization at 17.6 mT. We believe that the multi-tone irradiation can be extended to further enhance the 13C polarization at a low magnetic field.
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10
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van Zelst FHM, Romanuka J, Kentgens APM. Hyphenated structural identification of additives in transmission fluids. Analyst 2022; 147:2068-2073. [PMID: 35445223 PMCID: PMC9112864 DOI: 10.1039/d2an00323f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transmission fluids and other lubricants are used to reduce friction in engines and other surfaces. Additives in these transmission fluids are important for prolonging their lifetime and obtaining the desired physical properties for the lubricant. In this work, we show the successful structural identification of an important class of additives in transmission fluids by hyphenating several analytical techniques in-line. First, a separation of the additives in a transmission fluid was achieved within 10 minutes by using supercritical fluid chromatography. SFC-1H NMR was then used as a novel analysis method to structurally identify different additives in transmission fluids, in combination with mass spectrometry data. By this unique hyphenation of SFC, NMR spectroscopy and MS, several alkylated diphenylamines were identified, which are one of the most important classes of antioxidants. A novel hyphenated analytical method to unravel complex mixtures, SFC-1H NMR/MS, is introduced. It is applied for the structural analysis of additives in transmission fluids which can be used to prolong the lifetime of lubricants.![]()
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Affiliation(s)
- F. H. M. van Zelst
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- TI-COAST, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - J. Romanuka
- Shell Global Solutions International B.V., 1031 HW Amsterdam, The Netherlands
| | - A. P. M. Kentgens
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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11
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Saenz F, Tamski M, Milani J, Roussel C, Frauenrath H, Ansermet JP. Blatter-type radicals as polarizing agents for electrochemical overhauser dynamic nuclear polarization. Chem Commun (Camb) 2021; 58:689-692. [PMID: 34919627 DOI: 10.1039/d1cc05350g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Overhauser dynamic nuclear polarization (O-DNP) refers to a microwave-assisted process where an unpaired electron's (e.g. a radical) spin polarization is transferred to surrounding nuclei in solution, thus increasing the nuclear magnetic resonance (NMR) signal intensity of a given substance by several orders of magnitude. The presence of the unpaired electrons, which induces relaxation of the resulting hyperpolarized state when the radiation is halted, can be avoided by electrochemically removing the radicals on demand. We report the use of Blatter-type (benzo[e][1,2,4]triazinyl) radicals as polarizing agents, potentially opening the way to highly tunable radicals for electrochemical DNP.
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Affiliation(s)
- Felipe Saenz
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland.
| | - Mika Tamski
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland.
| | - Jonas Milani
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland.
| | - Christophe Roussel
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland. .,Section of Chemistry and Chemical Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Holger Frauenrath
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Jean-Philippe Ansermet
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland.
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